Sources within the human resource development ministry said they have received the resignation letter from the President's secretariat but would insist on a written letter of resignation from the VC as e-mail correspondence is not admissible.
Dattagupta's resignation came against the backdrop of the HRD ministry recommending his removal to the President last week "unconvinced" with the VC's reply on the show cause served on him.
However, Mukherjee had on September 23, returned the file of the HRD ministry recommending his sacking and asked it to seek a legal opinion before any decision can be taken.
The ministry had sent Dattagupta's file to the President after it allegedly found him guilty of financial and administrative wrongdoings.
Charges against Dattagupta, 68, included drawing salary from Visva Bharati and pension from Jawaharlal Nehru University simultaneously in alleged violation of the law.
Under the law, he was required to have got his pension amount deducted from the pay he received from Visva Bharati.
Besides this, Dattagupta was charged with making irregular appointments, including that of the Controller of Examinations despite having no powers, and sanctioning key posts in violation of the Visva Bharati Act.
Though the existing laws relating to Central Universities do not provide for sacking of a vice chancellor, the President can invoke section 16 of the General Clauses Act, 1987, to remove him.
The Act empowers the appointing authority to suspend or dismiss any person appointed under a Central act or regulation.
A three-member panel set up by the HRD ministry and headed by former Allahabad high court judge justice (retd) S S Yadav had allegedly found him guilty of the charges in February.
Senior Congress leader from West Bengal and Rajya Sabha MP Pradeep Bhattacharya had in June met the President to demand his removal, alleging the university was "losing its glory" under him.